AIM: The objective of the study was to determine if dairy goats selected as having either Low or High estimated breeding values for somatic cell count (EBV SCC) would differ in prevalence of intramammary infection (IMI).METHODS: The EBV SCC for all does in two dairy goat herds were calculated based on the three or four herd test results for somatic cell count (SCC) from the preceding lactations. Within each herd does were categorised into six age groups (i.e. 2, 3, 4, 5, 6 and >6 years old) and ranked on EBV SCC. Approximately the top (High group; n=149) and bottom (Low group; n=148) 12.5% of the does within each age group within each herd had milk samples collected from each gland on one calendar day for subsequent microbiology. The presence of any IMI or IMI due to a major pathogen at goat level was modelled using a GLM with a binomial link function.RESULTS: There was no difference between the High and Low groups in terms of age, days in milk at the time of sampling or in the proportion of the Saanen breed. Mean EBV SCC was -1.0 (SD 0.4) vs 0.8 (SD 0.4) for the Low and High groups, respectively, and there was no overlap in EBV SCC between groups. Goats in the Low group had lower prevalence of any IMI than those in the High group (0.67 (95% CI=0.58-0.76) vs 0.81 (95% CI=0.74-0.88); p=0.002). Goats in the High group were 8.4 (95% CI=1.9-38.0) times more likely to have IMI due to a major pathogen infection than goats in the Low group (p=0.006).CONCLUSIONS: Does with a high EBV SCC had a higher prevalence of any IMI and were more likely to have an IMI dueto a major pathogen than does with a low EBV SCC. Thus selection for EBV SCC is likely to result in a lower SCC and also lower prevalence of IMI.